The architecture of the SARS-CoV-2 RNA genome inside virion

Abstract

SARS-CoV-2 carries the largest single-stranded RNA genome and is the causal pathogen of the ongoing COVID-19 pandemic. How the SARS-CoV-2 RNA genome is folded in the virion remains unknown. To fill the knowledge gap and facilitate structure-based drug development, we develop a virion RNA in situ conformation sequencing technology, named vRIC-seq, for probing viral RNA genome structure unbiasedly. Using vRIC-seq data, we reconstruct the tertiary structure of the SARS-CoV-2 genome and reveal a surprisingly “unentangled globule” conformation. We uncover many long-range duplexes and higher-order junctions, both of which are under purifying selections and contribute to the sequential package of the SARS-CoV-2 genome. Unexpectedly, the D614G and the other two accompanying mutations may remodel duplexes into more stable forms. Lastly, the structure-guided design of potent small interfering RNAs can obliterate the SARS-CoV-2 in Vero cells. Overall, our work provides a framework for studying the genome structure, function, and dynamics of emerging deadly RNA viruses.

Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021

“…It is clear that the SARS-CoV-2 shares 81.9% nucleotide similarity to subgenus Sarbecovirus in the Betacoronavirus genus, previously found in China ( Wu et al, 2020 ). Similar to other coronaviruses, the novel SARS-CoV-2 virus is an enveloped, positive-sense-single-stranded RNA virus with a genome of approximately 30 kb encoding open reading frames ORF1a/b, spike (S), envelope (E), membrane (M), nucleocapsid (N), and several accessory proteins ( Cao et al, 2021 ; Sola et al, 2015 ). The papain-like (within nonstructural protein 3, nsp3) and 3C-like (nsp5) proteases auto-cleave ORF1a and ORF1b polyproteins divided into 16 nsps which are essential for viral replication and transcription.…”

Inhibition of SARS-CoV-2 coronavirus proliferation by designer antisense-circRNAs

“…To develop new RNA-based therapeutics for antiviral strategies, we designed and tested artificial small circRNAs containing antisense-RNA sequences that target SARS-CoV-2 RNA. We focussed on the 5′-UTR, because its RNA secondary structure is relatively well characterized and highly conserved ( 2 , 3 ), and there is evidence for important functions of the 5′-UTR on multiple levels, including viral genome replication ( 38 ) and transcription [subgenomic RNA (sgRNA) synthesis, ( 5 , 6 )], translational initiation ( 39 ), RNA stability ( 3 ) and, potentially, RNA packaging ( 40 ). To screen for functional antisense sequences and optimal SARS-CoV-2 targets in the 5′-UTR, we initially used two separate luciferase reporter systems (Figure 1A ).…”

RT-qPCR Detection of SARS-CoV-2: No Need for a Dedicated Reverse Transcription Step

“…The influence of RNA secondary structure on RT priming efficiency is an interesting, yet under-explored component of RT-qPCR sensitivity. Using the data from a recent publication that modelled the secondary structure of the SARS-CoV-2 genome [41], we surmised that the reverse primers from all six assays hybridise to regions of the genome projected to contain extensive secondary structures. Hence, we did not expect the minimal effect on priming efficiency that we observed.…”